BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472460.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 16,783,850 number of mapped reads = 16,635,932 (99.12%) number of supplementary alignments = 58,108 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,339,957 number of mapped paired reads (second in pair) = 8,295,975 number of mapped paired reads (both in pair) = 16,547,494 number of mapped paired reads (singletons) = 88,438 number of mapped bases = 1,632,637,030 bp number of sequenced bases = 1,632,446,306 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,573,451 duplication rate = 46.61% >>>>>>> Insert size mean insert size = 19,668.1048 std insert size = 1,381,776.4899 median insert size = 210 >>>>>>> Mapping quality mean mapping quality = 55.08 >>>>>>> ACTG content number of A's = 452,204,802 bp (27.7%) number of C's = 365,163,986 bp (22.37%) number of T's = 453,530,424 bp (27.78%) number of G's = 361,350,300 bp (22.14%) number of N's = 196,794 bp (0.01%) GC percentage = 44.5% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 8,784,200 number of insertions = 105,787 mapped reads with insertion percentage = 0.63% number of deletions = 81,860 mapped reads with deletion percentage = 0.48% homopolymer indels = 47.24% >>>>>>> Coverage mean coverageData = 0.5274X std coverageData = 13.2393X There is a 5.06% of reference with a coverageData >= 1X There is a 2.15% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.68% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.49% of reference with a coverageData >= 6X There is a 0.45% of reference with a coverageData >= 7X There is a 0.44% of reference with a coverageData >= 8X There is a 0.42% of reference with a coverageData >= 9X There is a 0.41% of reference with a coverageData >= 10X There is a 0.39% of reference with a coverageData >= 11X There is a 0.38% of reference with a coverageData >= 12X There is a 0.37% of reference with a coverageData >= 13X There is a 0.36% of reference with a coverageData >= 14X There is a 0.36% of reference with a coverageData >= 15X There is a 0.35% of reference with a coverageData >= 16X There is a 0.34% of reference with a coverageData >= 17X There is a 0.33% of reference with a coverageData >= 18X There is a 0.33% of reference with a coverageData >= 19X There is a 0.32% of reference with a coverageData >= 20X There is a 0.31% of reference with a coverageData >= 21X There is a 0.31% of reference with a coverageData >= 22X There is a 0.3% of reference with a coverageData >= 23X There is a 0.3% of reference with a coverageData >= 24X There is a 0.29% of reference with a coverageData >= 25X There is a 0.29% of reference with a coverageData >= 26X There is a 0.28% of reference with a coverageData >= 27X There is a 0.28% of reference with a coverageData >= 28X There is a 0.28% of reference with a coverageData >= 29X There is a 0.27% of reference with a coverageData >= 30X There is a 0.27% of reference with a coverageData >= 31X There is a 0.26% of reference with a coverageData >= 32X There is a 0.26% of reference with a coverageData >= 33X There is a 0.26% of reference with a coverageData >= 34X There is a 0.25% of reference with a coverageData >= 35X There is a 0.25% of reference with a coverageData >= 36X There is a 0.25% of reference with a coverageData >= 37X There is a 0.24% of reference with a coverageData >= 38X There is a 0.24% of reference with a coverageData >= 39X There is a 0.24% of reference with a coverageData >= 40X There is a 0.23% of reference with a coverageData >= 41X There is a 0.23% of reference with a coverageData >= 42X There is a 0.23% of reference with a coverageData >= 43X There is a 0.22% of reference with a coverageData >= 44X There is a 0.22% of reference with a coverageData >= 45X There is a 0.22% of reference with a coverageData >= 46X There is a 0.22% of reference with a coverageData >= 47X There is a 0.21% of reference with a coverageData >= 48X There is a 0.21% of reference with a coverageData >= 49X There is a 0.21% of reference with a coverageData >= 50X There is a 0.21% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 166365187 0.6674614744490446 15.239336468716276 chr2 243199373 127706015 0.5251083233672647 13.032599385593164 chr3 198022430 126439172 0.6385093446232328 11.230709885591153 chr4 191154276 54715709 0.286238477866956 10.21133447743903 chr5 180915260 73265528 0.40497152092089966 12.240712411959276 chr6 171115067 129631392 0.7575685430436117 15.226487285372684 chr7 159138663 103893997 0.6528520162319071 16.580744648546336 chr8 146364022 125075593 0.8545514894363863 19.062640288304696 chr9 141213431 63176809 0.4473852703146912 9.519915984650073 chr10 135534747 35533155 0.2621700765782224 7.0481339735662125 chr11 135006516 49457175 0.36633176283135843 9.643022297470573 chr12 133851895 80883029 0.6042725730554656 12.232808338266404 chr13 115169878 61492509 0.5339287500156942 17.01025077352096 chr14 107349540 42619869 0.39701957735450005 9.751795054516931 chr15 102531392 30902208 0.30139265055525627 7.6772289000132545 chr16 90354753 88304392 0.9773076575174745 22.85140747595539 chr17 81195210 67528650 0.8316826817739618 16.092598858044514 chr18 78077248 14027769 0.17966525920585727 4.628761620927203 chr19 59128983 32273003 0.545806833849992 9.980744836140659 chr20 63025520 52748047 0.8369315635951913 20.672829307237574 chr21 48129895 13559762 0.28173263207825405 14.10245006501691 chr22 51304566 15859692 0.3091282752494193 8.456773272436626 chrMT 16571 15121 0.9124977370104399 1.1495794457005821 chrX 155270560 76073429 0.4899411002317503 10.449940027869442 chrY 59373566 1089818 0.018355272782503918 1.0773513844195384